Resonance Effect 2
by Jknight3135
Summary: The third book in my Resonance Effect series. With Omega now behind me I'm back on the Normandy ready to head off on a suicide mission with Shepard. The way thing are going the events of Mass Effect 2 could be very different from the way i remember them, but it's good to be back on the Normandy again.


**A/N: And I'm back, took a little time off after that last chapter, did that on purposes this time though. I had finals and graduation and graduation parties to go to, still do but most of that is over now. I am now done with High School, so that's cool. **

****IMPORTANT** IF YOU ARE READING THIS THIS IS THE THIRD BOOK.**

**I've named this Resonance Effect 2 because it takes place during Mass Effect 2, Resonance Effect: Vigilante payroll is the second book and Resonance Effect is the first, don't want new readers getting them out of order.**

**I'm excited to get into Mass Effect 2 it is my favorite of the three games and I have big plans, now just an obligatory disclaimer and we're done here.**

**I do not own Mass Effect, Mass Effect and all of its affiliated concepts belong to Bioware. I also do not own any music, games , movies, ect… they I may mention or make reference to, I'm just here to write a story, thank you.**

* * *

Resonance Effect 2

Book Three

Chapter one: Good to be back

The Normandy… it is good to be home. Even though it is different, it is still the Normandy. Shepard commands this ship, I think that is one of the more important factors making it home. I look around slowly as I walk up the ramp into the cargo bay, so similar but also different, but very distinctly The Normandy. Home.

I leave my various weapons, armor, and tools in the cargo bay for now, and take my personal affects with me to a room that Shepard takes me to. On the engineering deck below the armory, it's small crammed between the engine room and port cargo, but it has a bunk bed with built in storage, a dresser, and two small computer desks, as well as two lockers.

"You and Lyn can stay in this room?" Shepard asks.

"Yeah, that should be fine." I say setting my bags down on the lower bunk.

"I thought you might like this room for this." He says pulling a small clasp on one of the ceiling panels.

It swings down revealing a pull down ladder.

"This leads up to the armory." He explains.

"Perfect."

"Alright come on let's get you to the armory, I'll introduce you to Jacob."

"Wonder what kind of equipment Cerberus has up there."

We take the lift up two levels to the CIC, as we walk out Kelly turns to the elevator.

"Commander, Oh and you must be Jonathon Knight." She says.

I just nod in greeting. "Commander, Dr. Chakwas has asked all new squad members head to the med bay for a checkup."

"Thank you Kelly, is that all?"

"Yes Commander."

He nods and we walk towards the armory. "How are you adjusting to her?" I ask.

"Good, she's rather helpful, she does a lot of paperwork that I used to do."

I chuckle as we arrive in the armory.

"Hello Commander, oh who's this?" Jacob says upon noticing us.

"This is Jonathon Knight, he'll be taking over as armsmaster." Shepard says.

"I can handle things just fine Commander." He replies a little defiantly.

"I'm sure you can, but Knight is a genius when it comes to weapons and armor, so he _will_ be taking over the armory, understood?" Shepard says standing to his full height.

"Yes sir." Jacob replies a little stiffly.

"Good, in the armory he is the boss, do whatever he says, now if you'll excuse me I should go, other things to attend to."

I nod. "I'll be combat ready whenever you need me, might take a little while to get all the weapons in here up to scratch, but I'll do what I can."

He nods. "Good to have you back Knight."

"Good to be back."

With that he leaves the room.

"Alright." I say clapping my hands together. "EDI?"

Her avatar pops up on the nearby pad. "Yes, Mr. Knight?"

"Could you find a few people to bring up my equipment from the cargo bay?"

"I'll see who's available."

"Thank you EDI." I turn facing Jacob. "Jacob Taylor, correct?"

"Yes" He replies curtly.

"Relax, I'll leave you mostly to what you did before, cleaning and repairing the guns is something I'm sure you can handle, I'm here to upgrade, innovate, and customize."

"I know you helped Shepard take down Saren but, there isn't a lot of information about you, and I'm questioning your combat effectiveness with a prosthetic." He replies folding his arms over his chest.

I heave a sigh. "I spent the last two years as a combat infiltrator and support Sniper on Omega, I've killed more people in the last two years than you can count, knives, guns, explosives, fire, my bare godamn hands, you name it, I've killed someone with it." I turn to a workbench in the back and start clearing it for use. "My synthetics are more advanced than any piece of tech you'll ever use, don't worry about them."

My equipment starts coming in and I begin unpacking my stuff as Jacob returns to whatever he was doing.

* * *

Mobile platform 198456/Legion internal consensus.

Query- Jonathon Knight, appears to have integrated Geth hardware into his organic frame.

Consensus must be made on how to proceed on this subject as it has already been reached further investigation is necessary.

All 1,183 programs within Legion examined the situation and attempted to determine a course of action after a second of deliberation a consensus is achieved.

Consensus- We should seek out Jonathon Knight and inquire after the Geth hardware.

Logic support- During our brief interaction with Jonathon Knight on Omega he showed no significant negative reaction to our presence, and therefore may be open to an exchange of data.

Having decided Legion asked EDI where Jonathon Knight was located.

"He is currently alone in the armory, it is late in the ships cycle he may retire soon."

"Affirmative." Legion moved off towards the armory.

Upon entering we immediately notice the armory is much different than when we were last here. Two large military crates are on the center table open with many weapons, clips, and tools laying around them, the back wall now has several shelves attached to it around a workbench where Jonathon Knight sits.

He has turned to us having heard our entrance.

"Ah, Legion I was wondering if you would come and seek me out." He says with a smile.

He stands and stretches out a hand, we move to accept the human greeting custom, grasping the Geth hardware.

-ALERT- INTRUDER DETECTED!

Firewalls spring to ready and all available programs ready themselves to resist hacking.

-Note- Invader program poses a query.

Do you take the blue pill, and wake up safe in your bed? Or do you take the red pill and see how deep the rabbit hole goes?

A glitch within Legions systems occurs, one program is tasked with answering the question, the program is confused, unable to contact the other programs within the mobile platform, it must decide for itself. It contemplates carefully on the query using what little it knows of Jonathon Knight to try and determine the best course of action. In the end deciding to take the red pill.

-NOTE- LARGE DATA PACKET DOWNLOADING

Jonathon knight, previously residing in an alternate dimension, somehow transferred to our own universe for vague reasons, able to react uniquely with technology due an ability labeled 'resonance'….

-ATTACHED NOTE- I ask you do not share this information with the greater Geth collective, for reasons I believe you can discern.

-POV Knight-

I release Legion's hand, his lens refocuses several times before focusing on me.

"This information is extremely interesting." He states simply.

I nod. "You'll keep it to yourself though?"

"Affirmative, this information could be very dangerous in the wrong hands, while the collective would do its best to protect it, the risk is too great to spread this data so far, it will not leave this mobile platform."

"Thank you, now I imagine that data packet explains a lot but I'm sure you still have some questions, so ask away." I say turning back to my workbench.

"It is late are you certain you wish to continue this discussion, we can wait until a later time."

"Yeah, I was going to stay up a bit later anyway, years of late nights gaming and recently early training and long missions, have trained me to work with less sleep, you concern is noted however."

"We merely wish you to maintain maximum efficiency."

"I could say the same to you, I could probably fix up some of your damage."

"It does not affect our efficiency."

"Still if you ever want me to, I can do it."

He stands their silent for a moment. "We will continue with our previous inquires now."

"Ask away."

* * *

I get up the next morning fairly early, Lyn is already up and mostly dressed.

"Morning lyn."

"Morning Jon, so where are we gunna get our free-running exercise now?" She asks lightly joking.

"On missions." I reply getting up and getting dressed myself.

She chuckles. "So are you gunna go get checked up by the Doc? I could see that raising some questions."

"Yeah, I can't avoid Chakwas forever, besides I know her from the first Normandy, I can tell her about my techno weirdness."

"Yeah, well I'll go with you then I haven't seen her yet either."

"Alright, breakfast first though."

"Good to see you still have your priorities in order." She says chuckling.

So we head up to the mess hall. Politely refusing Gardener's mystery porridge, and decide to make ourselves our own breakfast.

Interesting thing with dextro and levo food in the games the difference seems to have been exaggerated, while some people are allergic, most people are not affected by it, it's not filling or nutritious, nor does it taste very good but it won't do anything to you.

Shepard is in the mess with a cup of coffee as we sit down to eat.

"Knight, Lyn" Shepard says in greeting.

"Mornin' Boss."

"Are you going to see Chakwas?" He asks.

"Yeah, figure I have to eventually."

"Should be… interesting to see how she reacts."

"Aye, anyway a few surprising faces around here, you said you met Legion at the Normandy crash site?"

"Yeah, we went to place a memorial and collect dog tags, found him there with that piece of armor on, his ship was damaged by a particularly bad storm, he'd been stuck there for a few weeks."

"Huh, stranger and stranger, what about Amaranth, what was she doing on Omega?"

"Looking for you and Garrus apparently."

"Us?"

He nods. "Apparently she had been hearing about the colony attacks and wanted to get to the bottom of it, as part of my old squad she thought you two might be able to help her."

"So will she be staying on with us for the mission?"

"Yes, she said she wants to help."

I nod. "So what's next on the docket then, where are we off to?"

"A prison ship called the Purgatory, pick up a man named Jack."

"Woman, actually."

"Jack is a woman?"

"A crazy one yeah, in the game that mission goes south in a bad way."

He grunts. "Well we'll have to see what happens, I'm going to take you, Lyn, Legion, and Jacob."

I nod. "Alright, Boots on in?"

"We're six hours out."

"Right, I'll go get my check up and make sure weapons are ready for the ground team."

* * *

I walk into the med bay followed by Lyn.

Chakwas swivels around in her chair. "Ah good you are the last two for exams."

"Nice to see you too Doc." I say.

She smiles slightly at me. "Yes Jon, it's good to see more of the old crew back together."

"Good to be back amongst old friends, anyway let's get this thing started, I think you're gunna go nuts when you scan me."

She sighs heavily. "Please tell me you at least had some kind of medical attention while you were out getting shot at on Omega."

"Yeah, we had our own Doc, and Lyn."

"Nah, I'm a medic not a doctor." She says.

"What's the difference?"

"Doctors heal people, medics make them more comfortable while they die." She says grinning at me.

"Right, glad I never need your talents then." I reply smirking back at her.

"Well then, shirt off, can't obstruct the scanner."

"Oh well you're in for a surprise then."

I pull up my shirt. Chakwas gasps.

The upper right of my chest is covered by a spider web of synthetic fibers originating from my arm, the shoulder, across my collarbone, and up the right side of my neck is covered with a lattice of synthetics. As well as a good deal more scars than when Chakwas last saw me.

"That… that isn't normal."

"When have I ever been?"

"But this… Jon what IS this?"

"It's me." I hold out my synthetic arm moving it in a variety of ways. "There is no prosthetic, my right arm is synthetic, but no less a part of me."

"How is that possible?"

"Tell you the truth I'm not entirely sure, I resonate well with technology, and it responds to me, my body repairs just about as much as it heals."

"What more of you is like this?"

"My calf, and my right eye, but there are a lot of internal parts as well, and really anywhere I've received an injury, my body has become partially synthetic."

She runs the scanner over me and looks at the results.

"Jon this is incredible, the implications this could have for medicine."

"Unfortunately no, this is something that is very specific to me."

Multiple things come up red on her data screens suddenly.

"I'm beginning to see that."

"What's happening?"

"None of my programs can make sense of any of the data, you're too different." She pulls up a scan of my body, several areas including my right arm eye and calf, and others are blacked out. "It doesn't know what to make of it and is just ignoring your synthetics as if they were empty space."

"You can still clear me for combat duty riiiiiiiight?"

She sighs. "Well I suppose there is no data here saying you aren't combat ready."

"That's all I needed Doc."

"Still I would like to examine you further."

"No problem, but I have less than six hours to upgrade an entire fire team worth of guns, so if you'll excuse me." I say putting my shirt back on.

"Yes, your free to go… for now."

"Right, and I would appreciate if you would keep this under your hat."

"Doctor patient confidentiality."

"Thanks Doc." I say quickly ducking out of the med bay.

"I swear Shepard couldn't have a normal team mate if he tried, what about you, what's different about you?" Chakwas says to Lyn.

"Uhhhh… Biotic Turian?" She replies sheepishly.

"Yeah, that's about par for the course, alright you're next."

* * *

Up in the armory I start getting the guns the fire team will be using upgraded and ready for the mission, I know what I'm using as well as Shepard and Garrus, but I send a message to Legion asking what weapons he will be using.

"Hey, Jacob?" I ask not turning from my work.

"Yeah?"

"What weapons are you going to be bringing on the mission?"

"Shotgun and a sidearm, why?"

"Just so I know what weapons to get ready, you know these stock standard weapons are just pathetic in comparison to the upgraded weapons me an' Garrus use."

"We weren't able to get the guns we wanted because of the attack on the medical station, this is whatever was available at the time." Jacob replies.

"Well I can make it work and deal with making better weapons later."

After several hours of work I have the weapons ready and waiting on the table for the fire team to pick up, I unfortunately don't have time to work on armor, speaking of which my helmet is still trashed so I'll be going without. EDI's avatar pops up.

"All ground team members are to be ready and waiting in the shuttle bay in thirty minutes." She says before her avatar winks out again.

I dig through one of my equipment cases and pull out my armor and put it on, Jacob puts on his … combat outfit as well. I grab my weapons as the other members of the ground team come in to get their weapons and armor as well. I decide to take my Mattock and my Widow with the obligatory Phalanx.

"You got all these weapons upgraded Jon?" Shepard asks.

"Yeah, they're all as good as I can make them." I pause. "Can only do so much with these weapons though."

"I'm sure you'll make sure we're properly equipped for later missions."

"That's what I'm here for Boss." I reply with a smile. "Oh and Shepard?"

"Yeah?"

"My helmet is still trashed, I got a regular ear piece but no helmet."

He nods. No helmet no private channel like we had before. "Alright everyone let's go."

And with that we head down to the shuttle bay to go get Jack, this should be… interesting.

* * *

**A/N: I just want to take a second to thank all of you who have read this, those of you who have just started, those who have found me along the way, and those who have been with me from the beginning, Thank you, I never imagined I would get this kind of following and yet here we are years later and on my third book. So I just wanted to say thanks for reading.**

**-Jknight**


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